Search

The SARS-CoV-2 Omicron variant (B.1.1.529) has multiple spike protein mutations1,2 that contribute to viral escape from antibody neutralization3–6 and reduce vaccine protection from infection7,8. The extent to which other components of the adaptive response such as T cells may still target Omicron and contribute to protection from severe outcomes is unknown. Here we assessed the ability of T cells to react to Omicron spike protein in participants who were vaccinated with Ad26.CoV2.S or BNT162b2, or unvaccinated convalescent COVID-19 patients (n = 70). Between 70% and 80% of the CD4+ and CD8+ T cell response to spike was maintained across study groups. Moreover, the magnitude of Omicron cross-reactive T cells was similar for Beta (B.1.351) and Delta (B.1.617.2) variants, despite Omicron harbouring considerably more mutations. In patients who were hospitalized with Omicron infections (n = 19), there were comparable T cell responses to ancestral spike, nucleocapsid and membrane proteins to those in patients hospitalized in previous waves dominated by the ancestral, Beta or Delta variants (n = 49). Thus, despite extensive mutations and reduced susceptibility to neutralizing antibodies of Omicron, the majority of T cell responses induced by vaccination or infection cross-recognize the variant. It remains to be determined whether well-preserved T cell immunity to Omicron contributes to protection from severe COVID-19 and is linked to early clinical observations from South Africa and elsewhere9–12.

Background Reports on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread across Africa have varied, including among healthcare workers (HCWs). This study assessed the comparative SARS-CoV-2 burden and associated risk factors among HCWs in three African countries. Methods A multicentre study was conducted at regional healthcare facilities in Côte d’Ivoire (CIV), Burkina Faso (BF) and South Africa (SA) from February to May 2021. HCWs provided blood samples for SARS-CoV-2 serology and nasopharyngeal/oropharyngeal swabs for testing of acute infection by polymerase chain reaction and completed a questionnaire. Factors associated with seropositivity were assessed with logistic regression. Results Among 719 HCWs, SARS-CoV-2 seroprevalence was 34.6% (95% confidence interval 31.2 to 38.2), ranging from 19.2% in CIV to 45.7% in BF. A total of 20 of 523 (3.8%) were positive for acute SARS-CoV-2 infection. Female HCWs had higher odds of SARS-CoV-2 seropositivity compared with males, and nursing staff, allied health professionals, non-caregiver personnel and administration had higher odds compared with physicians. HCWs also reported infection prevention and control (IPC) gaps, including 38.7% and 29% having access to respirators and IPC training, respectively, in the last year. Conclusions This study was a unique comparative HCW SARS-CoV-2 investigation in Africa. Seroprevalence estimates varied, highlighting distinctive population/facility-level factors affecting COVID-19 burden and the importance of established IPC programmes to protect HCWs and patients.

The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively1–3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

SummaryThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants respectively1–3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

We report the first whole genome constellations of Mozambican rotavirus A strains detected between 2012 and 2013 in the Mavalane General Hospital in Maputo city and Manhiça District Hospital in the Manhiça district. Consensus sequences for ten DS-1-like strains (G2P[4] and G8P[4]) were identified with an Illumina Miseq platform using cDNA prepared from dsRNA extracted from stool samples, without genome amplification or prior adaptation to cell culture. Comparison of previously reported genotyping results and the consensus sequences described in this study, indicated that the genotype primers specific for G12 and P[4] might require revision. Phylogenetic analyses indicated diversity among the G2P[4] Mozambican strains and suggested reassortment between G2P[4] and G8P[4] Mozambican strains, as well as the intragenogroup reassortment of all the genome segments encoding VP1, 2, 3 and 6 for strain RVA/Human-wt/MOZ/0045/2012G8P[4]. These results highlight the necessity to determine whole genome constellations to confirm surveillance data in Africa and to monitor the growing diversity in DS-1-like strains.

The SARS-CoV-2 Omicron variant escapes neutralizing antibodies elicited by vaccines or infection. However, whether Omicron triggers cross-reactive humoral responses to other variants of concern (VOCs) remains unknown. We use plasma from 20 unvaccinated and seven vaccinated individuals infected by Omicron BA.1 to test binding, Fc effector function and neutralization against VOCs. In unvaccinated individuals, Fc effector function and binding antibodies target Omicron and other VOCs at comparable levels. However, Omicron BA.1-triggered neutralization is not extensively cross-reactive for VOCs (14 to 31-fold titer reduction) and we observe 4-fold decreased titers against Omicron BA.2. In contrast, vaccination followed by breakthrough Omicron infection was associated with improved cross-neutralization of VOCs, with titers exceeding 1:2,100. This has important implications for vulnerability of unvaccinated Omicron-infected individuals to reinfection by circulating and emerging VOCs. While Omicron-based immunogens may be adequate boosters, they are unlikely to be superior to existing vaccines for priming in SARS-CoV-2 naive individuals.

Mozambique introduced the Rotarix&reg, vaccine (GSK Biologicals, Rixensart, Belgium) into the National Immunization Program in September 2015. Although G1P[8] was one of the most prevalent genotypes between 2012 and 2017 in Mozambique, no complete genomes had been sequenced to date. Here we report whole genome sequence analysis for 36 G1P[8] strains using an Illumina MiSeq platform. All strains exhibited a Wa-like genetic backbone (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). Phylogenetic analysis showed that most of the Mozambican strains clustered closely together in a conserved clade for the entire genome. No distinct clustering for pre- and post-vaccine strains were observed. These findings may suggest no selective pressure by the introduction of the Rotarix&reg, vaccine in 2015. Two strains (HJM1646 and HGM0544) showed varied clustering for the entire genome, suggesting reassortment, whereas a further strain obtained from a rural area (MAN0033) clustered separately for all gene segments. Bayesian analysis for the VP7 and VP4 encoding gene segments supported the phylogenetic analysis and indicated a possible introduction from India around 2011.7 and 2013.0 for the main Mozambican clade. Continued monitoring of rotavirus strains in the post-vaccine period is required to fully understand the impact of vaccine introduction on the diversity and evolution of rotavirus strains.

Rotavirus A (RVA) is an important pathogen causing gastroenteritis in many species, including humans and pigs. The objective of this study was to determine the prevalence of RVA in pigs from smallholdings and commercial farms in southern Mozambique and characterize the complete genomes of selected strains. RVA was detected at a rate of 11.8% (n = 288), of which 7.6% was detected at commercial farms and 4.2% at smallholdings. The whole genomes of eight rotavirus strains were determined using an Illumina MiSeq platform. Seven displayed a G9P[13] and one a G4P[6] genotype combination, all with a typical porcine backbone (I1/5-R1-C1-M1-A1/8-N1-T1/7-E1-H1). Phylogenetic analysis indicated that the seven G9P[13] strains were in fact one strain that circulated on a commercial pig farm. The genome segments of this strain clustered with diverse segments of human and porcine RVA strains from various Asian countries. Analysis of the G4P[6] strain revealed four distinct genome segments (VP2, VP4, VP6 and VP7) and five genome segments closely related to South African porcine rotavirus strains (NSP1, NSP3, NSP4, NSP5 and VP1). These results suggest that both the G4P[6] and the G9P[13] strains possibly emerged through multiple reassortment events. The presence of these strains on the commercial farms and smallholdings calls for a more in-depth surveillance of rotavirus in Mozambique.

Human rotavirus A (RVA) causes acute gastroenteritis in infants and young children. The broad use of two vaccines, which are based on RVA strains from Europe and North America, significantly reduced rotavirus disease burden worldwide. However, a lower vaccine effectiveness is recorded in some regions of the world, such as sub-Saharan Africa, where diverse RVA strains are circulating. Here, a plasmid-based reverse genetics system was used to generate simian RVA reassortants with VP4 and VP7 proteins derived from African human RVA strains not previously adapted to cell culture. We were able to rescue 1/3 VP4 mono-reassortants, 3/3 VP7 mono-reassortants, but no VP4/VP7 double reassortant. Electron microscopy showed typical triple-layered virus particles for the rescued reassortants. All reassortants stably replicated in MA-104 cells, however, the VP4 reassortant showed significantly slower growth compared to the simian RVA or the VP7 reassortants. The results indicate that, at least in cell culture, human VP7 has a high reassortment potential, while reassortment of human VP4 from unadapted human RVA strains with simian RVA seems to be limited. The characterized reassortants may be useful for future studies investigating replication and reassortment requirements of rotaviruses as well as for the development of next generation rotavirus vaccines.

In Mozambique rotavirus (RV) was shown to be the greatest cause of acute diarrhoea in infants from 0 to 11 months, and in 2015, national rotavirus vaccination was introduced. As with other developing countries, there is very limited active strain characterisation. Rotavirus positive clinical specimens, collected between 2012 and 2013, have now provided information on the genotypes circulating in southern Mozambique prior to vaccine introduction. Genotypes G2 (32.4%), G12 (28.0%), P[4] (41.4%) and P[6] (22.9%) (n = 157) strains were commonly detected with G2P[4] (42.3%) RVs being predominant, specifically during 2013. Phylogenetic evaluation of the VP7 and VP8* encoding genes showed, for the majority of the Mozambican strains, that they clustered with other African strains based on genotype. RVA/Human-wt/MOZ/0153/2013/G2P[4], RVA/Human-wt/MOZ/0308/2012/G2P[4] and RVA/Human-wt/MOZ/0288/2012/G12P[8] formed separate clusters from the other Mozambican strains with similar genotypes, suggesting possible reassortment. Amino acid substitutions in selected epitope regions also supported phylogenetic clustering. As expected, the VP7 and VP8* genes from the Mozambican strains differed from both the RotaTeq® (SC2-9) G2P[5] and Rotarix® (A41CB052A) G1P[8] genes. This study provides information on the genetic diversity of rotavirus strains prior to vaccine introduction and generates baseline data for future monitoring of any changes in rotavirus strains in response to vaccine pressure. Electronic supplementary material The online version of this article (doi:10.1007/s00705-017-3575-y) contains supplementary material, which is available to authorized users.

We report the first description of rotavirus A strains in African buffalo (Syncerus caffer). Following RNA extraction from stool samples, cDNA was prepared, followed either by sequence-independent amplification and 454 pyrosequencing or direct sequencing on an Illumina MiSeq platform. RVA/Buffalo-wt/ZAF/4426/2002/G29P[14] exhibited a novel G29P[14] combination and an artiodactyl backbone: I2-R2-C2-M2-A11-N2-T6-E2-H3. RVA/Buffalo-wt/ZAF/1442/2007/G10P[11] also exhibited an artiodactyl backbone: I2-R2-C2-M2-A13-N2-T6-E2-H3. Characterisation of these genome constellations indicate that the two buffalo strains are moderately diverse from each other and related to South African bovine RVA strains. The detection of RVA in buffalo contribute to our understanding of the host range of rotavirus in animals.

A high prevalence of G12 rotavirus strains has previously been reported in southern Mozambique. In this study, the full genomes of five Mozambican G12 strains were determined directly from stool using an Illumina Miseq platform. One sample (0060) contained an intergenogroup co-infection of a G12P[8] Wa-like strain and a GXP[14] DS-1-like strain. The sequences of seven genome segments, detected for the GXP[14] strain, clustered with a diverse group of mostly animal strains, suggesting co-infection with a strain of possible animal origin. The stool samples contained G12P[6] rotavirus strains with Wa-like backbones. Phylogenetic analyses of the VP4 and VP7 encoding segments of the G12P[6] strains suggested that they were reassortants containing backbones that are similar to that of the G12P[8] strain. The study confirms previous observations of interspecies transmission and emphasizes the importance of whole-genome sequencing in order to evaluate rotavirus co-infections and reassortants.

Listeria monocytogenes can grow and multiply in various food matrices and cause severe human illness. Apart from the influence on consumer health, L. monocytogenes contamination of ready-to-eat (RTE) food products causes major economic losses due to product recalls. Control of foodborne pathogens in RTE food products is a challenge, specifically in foods that cannot undergo a heat-treatment during processing. The aim of this study was to develop control strategies for the management of L. monocytogenes in an avocado processing facility, additional to a quality control system. An in-house monitoring system (IMS) was established to test specifically for Listeria spp. in the final products and processing environment, including floors, equipment, work areas and personnel. Guacamole and environmental samples were collected and tested on-site for Listeria with the ISO 11290-1 method. Based on the prevalence of Listeria, the facility introduced new strategies in processing to counter cross contamination. Results from the 2014 guacamole production season showed almost complete eradication of Listeria spp. in final products (0.17%, n = 1170) and the processing facility (0.79%, n = 1520). This is a major achievement since the highest incidence of Listeria spp. over a period of five years was measured at 11.39% (n = 948) in the final product during the 2013 season and 13.44% (n = 1927) in the processing facility in 2011. These results indicate that successful management of Listeria spp. in an avocado processing facility can be accomplished with in-house monitoring of the listerial population and subsequent adjustments to the processing system.

Listeria monocytogenes is a growing concern in the food industry as it is the causative agent of human listeriosis. There are many research articles concerning the growth, survival, and diversity of L. monocytogenes strains isolated from food-related sources, elucidating the difficulty in controlling these bacteria in a food-processing facility. Bacteriophage biocontrol of L. monocytogenes strains was introduced in 2006, through the first commercial bacteriophage product targeting L. monocytogenes ListShieldTM. This review focuses on the use of bacteriophage biocontrol to target L. monocytogenes in the food industry, specifically direct application of the bacteriophages to food products. In addition, we discuss characteristics of these bacteria that will have a significant influence on the effective treatment of bacteriophages such as genetic diversity between strains prevalent in one facility. There are many positive results of phage treatments targeting L. monocytogenes in food; however, success of in vitro studies might not be reproducible in practice. Future studies should focus on creating experimental design that will imitate the conditions found in the food industry, such as a stressed state of the targeted bacteria. In situ evaluation of bacteriophage treatment of L. monocytogenes will also be necessary because the presence of these bacteria in a processing facility can vary greatly regarding genetic diversity. The potential use of phages in the food-processing facility as a biosanitizer for L. monocytogenes, as well as the use of lysins to target these bacteria should also be explored. Despite the exciting research avenues that have to be explored, current research shows that biocontrol of L. monocytogenes is feasible and has potential to positively impact the food industry.

The aim of this study was to subtype Listeria monocytogenes strains present in an avocado processing facility using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLPs) and pulsed-field gel electrophoresis (PFGE). The inlA gene of the L. monocytogenes isolates was PCR amplified and cut with the restriction endonuclease Alu I or Tsp 509I. Initial investigation of 64 L. monocytogenes isolates indicated that Alu I was more discriminating and therefore an additional 76 isolates were subtyped with PCR-RFLPs using Alu I. The PCR-RFLP with Alu I resulted in three banding patterns. Subtyping of the isolates using PFGE was carried out by macrorestriction of the genomic DNA with Apa I and Asc I. The PFGE fingerprints generated by Apa I contained 5 clusters and resulted in better differentiation between the strains than digestion with Asc I. The majority of strains were grouped in cluster I ( n = 22) and in cluster II ( n = 50). All of the clusters contained product, as well as environmental isolates and thus no correlations with specific sources of contamination could be established. The results of this study indicated that both molecular subtyping methods, PCR-RFLP and PFGE, were sensitive and specific enough to assess the diversity among the majority of the L. monocytogenes isolates. This is the first study in which L. monocytogenes isolates from a South African avocado processing facility were characterised with PCR-RFLP and PFGE. Results clearly point to the need for increased hygienic measures to prevent the dissemination of this pathogen during avocado processing.

Enterobacter sakazakii has recently been reclassified as the novel genus Cronobacter . These bacteria have been associated with disease outbreaks and sporadic infections, particularly in premature and immunocompromised infants. Cronobacter spp. can cause foodborne infections such as neonatal meningitis, septicaemia and necrotising enterocolitis. Infant formula milk is the only food source that has been epidemiologically linked to disease outbreaks caused by Cronobacter spp. This holds particular risk for premature and immunocompromised infants. This review focuses on the recent reclassification of Cronobacter and the importance that these pathogens pose to the food industry. The inactivation, inhibition, thermal, osmotic and desiccation tolerances of these bacteria are described, as well as improvements made in the isolation and detection methods of members of Cronobacter from food products.

Members of the genus Cronobacter are opportunistic pathogens associated with life-threatening infections in immuno-compromised individuals. Polyphasic analysis has facilitated the classification of the novel genus Cronobacter containing five species. However, since this recent reclassification there are not many identification methods optimised for differentiation between the five Cronobacter species. This differentiation between the species is of importance as there are indications that the species may be diverse regarding their virulence. The aim of this study was to develop a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) protocol to differentiate between the five Cronobacter species. The rpoB gene of 49 Enterobacteriaceae strains, including 33 Cronobacter strains was amplified using conventional PCR, followed by digestion of these PCR products with restriction endonucleases MboI, HinP1I and Csp6I. The PCR-RFLP analysis with single digestions of each of the restriction endonucleases did not distinguish between all five Cronobacter species. This study describes the successful differentiation of the five Cronobacter species based on the amplification of the rpoB gene followed by the combined digestion with restriction endonucleases Csp6I and HinP1I. This PCR-RFLP assay is an accurate identification method that ensures rapid differentiation between the five species of Cronobacter.

The reclassification of the genus Cronobacter (previously known as Enterobacter sakazakii) was based on a polyphasic analysis that led to the description of five species. These bacteria are opportunistic pathogens that can cause neonatal meningitis and other infections in immuno-compromised individuals. Cronobacter species have been reported to show differences in sensitivity to antibiotics, heat and chemicals, as well as differences in virulence. The objective of this study was to classify Cronobacter isolates from infant formula milk, the food processing environment and fresh produce in South Africa and to evaluate the phylogenetic placement of these isolates based on the rpoA and 16S ribosomal RNA (rRNA) gene sequences. All the South African strains were identified as Cronobacter sakazakii despite the wide variety of isolation sources. No relation between the phylogenetic placement and strain origin could be determined. Strains of C. sakazakii, Cronobacter dublinensis, Cronobacter turicensis and Cronobacter muytjensii could be differentiated from each other, but it was not possible to differentiate between C. sakazakii and Cronobacter malonaticus based on the rpoA and 16S rRNA gene sequences alone. However, sequence data of these two genes can be used to differentiate between C. sakazakii and C. malonaticus when used in combination with biochemical analysis based on the utilisation of malonate.

PurposeThe paper sets out to explore the leadership processes and dynamics of change management in a fragmented, and resource‐poor, health service in an impoverished rural region in South Africa.Design/methodology/approachThe paper outlines an action research process aimed at assisting the stakeholders of two rural clinics to integrate psychiatric care into the Primary Health Care service that they offer their respective communities. This involved the transformation of existing practices through a form of praxis that involved learning from action and acting on learning.FindingsThe findings of the paper relate to the role of leadership in the facilitation of transformational learning in team‐based social action. Four areas of leadership responsibility are highlighted: the transformation of inappropriate mental models; the development of strategic resilience; the shifting of the locus of control of stakeholders to a more internal position; and the creation of a social environment in which intangible capital resources are generated and leveraged in the collective interest.Research limitations/implicationsThis paper is subject to the limitations of potential bias and distortion in action research. Although the “objective” evidence of the integration of psychiatric services at Pelsrus and Kwanomzamo clinics exists, the portrayal of the learning processes through which this was achieved could have been influenced unwittingly by the authors' own knowledge and other interests.Practical implicationsThe paper endorses the educational importance of work‐based projects through which strong tacit leadership knowledge bases can be developed in health sector personnel.Originality/valueThis paper has attempted to share the effectiveness of work‐ and project‐based learning in district health teams in South Africa. In particular, it has outlined how the learning strategy of the module leverages the team structure of the district health management units in order to create and exploit the social and morale capital resources that are potentially available through such a structure and the covenantal culture that it spawns. Furthermore, an attempt has been made to show how these resources are leveraged in the generation of mission‐pertinent tacit knowledge that is then converted by project stakeholders into explicit knowledge forms that can be used more effectively in framing subsequent strategic action.

The Beta variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in South Africa in late 2020 and rapidly became the dominant variant, causing over 95% of infections in the country during and after the second epidemic wave. Here we show rapid replacement of the Beta variant by the Delta variant, a highly transmissible variant of concern (VOC) that emerged in India and subsequently spread around the world. The Delta variant was imported to South Africa primarily from India, spread rapidly in large monophyletic clusters to all provinces, and became dominant within three months of introduction. This was associated with a resurgence in community transmission, leading to a third wave which was associated with a high number of deaths. We estimated a growth advantage for the Delta variant in South Africa of 0.089 (95% confidence interval [CI] 0.084-0.093) per day which corresponds to a transmission advantage of 46% (95% CI 44-48) compared to the Beta variant. These data provide additional support for the increased transmissibility of the Delta variant relative to other VOC and highlight how dynamic shifts in the distribution of variants contribute to the ongoing public health threat.